ReFOLD3 Server
Refinement of 3D protein models using molecular dynamics simulations and quality assessment.
ReFOLD3 refines 3D protein models with molecular dynamics under gradual restraints derived from predicted per-residue quality and residue–residue contacts — improving accuracy beyond the starting model while guarding against over-refinement.
MD-based refinement
Restrained molecular dynamics relaxes and optimises the model toward the native state.
Quality-guided restraints
ModFOLD per-residue scores decide where to restrain tightly and where to let regions move.
Automated selection
Upload a PDB model; the server runs the protocol and returns the best-scoring refined structure.
- Upload PDB model
- Configure intensity
- Run refinement
- Download results
> key_publications
Peer-reviewed foundations
ReFOLD3: Refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
Nucleic Acids Research · 2021 · 22 citations
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process
Bioinformatics Advances · 2023 · 19 citations
Methods for the Refinement of Protein Structure 3D Models
International Journal of Molecular Sciences · 2019 · 80 citations